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Open data
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Basic information
Entry | Database: PDB / ID: 7nim | ||||||
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Title | X-ray crystal structure of LsAA9A - cinnamon extract soak | ||||||
![]() | Auxiliary activity 9 | ||||||
![]() | OXIDOREDUCTASE / Enzyme / Complex / Inhibitor | ||||||
Function / homology | ![]() cellulose binding / cellulase / cellulase activity / cellulose catabolic process / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Frandsen, K.E.H. / Tokin, R. / Skov, L. / Johansen, K.S. / Lo Leggio, L. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Inhibition of lytic polysaccharide monooxygenase by natural plant extracts. Authors: Tokin, R. / Frandsen, K.E.H. / Ipsen, J.O. / Lo Leggio, L. / Poojary, M.M. / Berrin, J.G. / Grisel, S. / Brander, S. / Jensen, P.E. / Johansen, K.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 78.3 KB | Display | ![]() |
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PDB format | ![]() | 55.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 17.1 KB | Display | |
Data in CIF | ![]() | 26 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ninC ![]() 5achS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein / Sugars , 2 types, 2 molecules A![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#1: Protein | Mass: 25272.850 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#3: Sugar | ChemComp-NAG / |
-Non-polymers , 6 types, 386 molecules ![](data/chem/img/CU.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/UFK.gif)
![](data/chem/img/UFN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/UFK.gif)
![](data/chem/img/UFN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CU / | ||
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#4: Chemical | ChemComp-ACT / | ||
#5: Chemical | ChemComp-UFK / | ||
#6: Chemical | ChemComp-UFN / | ||
#7: Chemical | ChemComp-CL / #8: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.23 Å3/Da / Density % sol: 61.97 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 3.5 M NaCl, 0.1 M citric acid pH 4.0. 20-25 mg/ml LsAA9A. 2 ul hanging drops (1:1 protein:reservoir ratio). |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 1, 2019 |
Radiation | Monochromator: SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→44.3 Å / Num. obs: 59727 / % possible obs: 100 % / Redundancy: 70.1 % / CC1/2: 0.999 / Rrim(I) all: 0.165 / Net I/σ(I): 20.57 |
Reflection shell | Resolution: 1.45→1.54 Å / Redundancy: 41.3 % / Num. unique obs: 9464 / CC1/2: 0.71 / Rrim(I) all: 1.846 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5ACH Resolution: 1.45→44.3 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.126 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.055 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 67.38 Å2 / Biso mean: 21.047 Å2 / Biso min: 12.05 Å2
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Refinement step | Cycle: final / Resolution: 1.45→44.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.538 Å / Rfactor Rfree error: 0 / Total num. of bins used: 9
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